{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T12:01:59Z","timestamp":1784894519094,"version":"3.55.0"},"reference-count":76,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2022,1,30]],"date-time":"2022-01-30T00:00:00Z","timestamp":1643500800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2017R1C1B2004597"],"award-info":[{"award-number":["NRF-2017R1C1B2004597"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hallym University Research Fund 2020","award":["HURF-2020-13"],"award-info":[{"award-number":["HURF-2020-13"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The vaginal microbiome plays an important role in women\u2019s health and disease. Here we reanalyzed 40 vaginal transcriptomes from a previous study of de novo assembly (metaT-Assembly) followed by functional annotation. We identified 286,293 contigs and further assigned them to 25 phyla, 209 genera, and 339 species. Lactobacillus iners and Lactobacillus crispatus dominated the microbiome of non-bacterial vaginosis (BV) samples, while a complex of microbiota was identified from BV-associated samples. The metaT-Assembly identified a higher number of bacterial species than the 16S rRNA amplicon and metaT-Kraken methods. However, metaT-Assembly and metaT-Kraken exhibited similar major bacterial composition at the species level. Binning of metatranscriptome data resulted in 176 bins from major known bacteria and several unidentified bacteria in the vagina. Functional analyses based on Clusters of Orthologous Genes (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways suggested that a higher number of transcripts were expressed by the microbiome complex in the BV-associated samples than in non-BV-associated samples. The KEGG pathway analysis with an individual bacterial genome identified specific functions of the identified bacterial genome. Taken together, we demonstrated that the metaT-Assembly approach is an efficient tool to understand the dynamic microbial communities and their functional roles associated with the human vagina.<\/jats:p>","DOI":"10.3390\/ijms23031621","type":"journal-article","created":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T01:46:08Z","timestamp":1643593568000},"page":"1621","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8416-5173","authenticated-orcid":false,"given":"Won Kyong","family":"Cho","sequence":"first","affiliation":[{"name":"College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeonhwa","family":"Jo","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4199-7033","authenticated-orcid":false,"given":"Seri","family":"Jeong","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, 1 Singil-ro, Yeongdeungpo-gu, Seoul 07441, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s40168-020-00875-0","article-title":"Microbiome definition re-visited: Old concepts and new challenges","volume":"8","author":"Berg","year":"2020","journal-title":"Microbiome"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s40168-015-0094-5","article-title":"The vocabulary of microbiome research: A proposal","volume":"3","author":"Marchesi","year":"2015","journal-title":"Microbiome"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Normandin, S., and Wolfe, C.T. (2013). Vitalism and the Scientific Image in Post-Enlightenment Life Science, 1800\u20132010, Springer.","DOI":"10.1007\/978-94-007-2445-7"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e00217-17","DOI":"10.1128\/mSystems.00217-17","article-title":"Earth microbiome project and global systems biology","volume":"3","author":"Gilbert","year":"2018","journal-title":"MSystems"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"S38","DOI":"10.1111\/j.1753-4887.2012.00493.x","article-title":"Defining the human microbiome","volume":"70","author":"Ursell","year":"2012","journal-title":"Nutr. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1093\/humrep\/del022","article-title":"Baseline dimensions of the human vagina","volume":"21","author":"Barnhart","year":"2006","journal-title":"Hum. Reprod."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4680","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"Ravel","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"S36","DOI":"10.1093\/infdis\/jiw184","article-title":"The vaginal microbiome: Current understanding and future directions","volume":"214","author":"Martin","year":"2016","journal-title":"J. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1146\/annurev-micro-092611-150157","article-title":"Vaginal microbiome: Rethinking health and disease","volume":"66","author":"Ma","year":"2012","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.tim.2016.11.007","article-title":"Lactobacillus iners: Friend or foe?","volume":"25","author":"Petrova","year":"2017","journal-title":"Trends Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.3389\/fmicb.2016.01936","article-title":"Lactobacilli dominance and vaginal pH: Why is the human vaginal microbiome unique?","volume":"7","author":"Miller","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1111\/j.1600-0463.2005.apm1130201.x","article-title":"Bacterial vaginosis\u2014A microbiological and immunological enigma","volume":"113","author":"Forsum","year":"2005","journal-title":"APMIS"},{"key":"ref_13","first-page":"271","article-title":"The female vaginal microbiome in health and bacterial vaginosis","volume":"11","author":"Chen","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"354","DOI":"10.3389\/fcimb.2020.00354","article-title":"Bacterial vaginosis: Current diagnostic avenues and future opportunities","volume":"10","author":"Redelinghuys","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1111\/mec.13739","article-title":"Life in leaf litter: Novel insights into community dynamics of bacteria and fungi during litter decomposition","volume":"25","author":"Purahong","year":"2016","journal-title":"Mol. Ecol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1007\/s00248-017-0996-9","article-title":"An 18S rRNA workflow for characterizing protists in sewage, with a focus on zoonotic trichomonads","volume":"74","author":"Maritz","year":"2017","journal-title":"Microb. Ecol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5029","DOI":"10.1038\/s41467-019-13036-1","article-title":"Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis","volume":"10","author":"Johnson","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e00271-18","DOI":"10.1128\/mSystems.00271-18","article-title":"Impact of preservation method and 16S rRNA hypervariable region on gut microbiota profiling","volume":"4","author":"Chen","year":"2019","journal-title":"Msystems"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"670336","DOI":"10.3389\/fmicb.2021.670336","article-title":"Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes","volume":"12","author":"Peterson","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1177\/1933719113488838","article-title":"Diversity of the vaginal microbiome correlates with preterm birth","volume":"21","author":"Hyman","year":"2014","journal-title":"Reprod. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1038\/s41591-019-0450-2","article-title":"The vaginal microbiome and preterm birth","volume":"25","author":"Fettweis","year":"2019","journal-title":"Nat. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"9212","DOI":"10.1038\/s41598-017-07790-9","article-title":"The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women","volume":"7","author":"Freitas","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"24380","DOI":"10.1038\/srep24380","article-title":"Effects of low dose estrogen therapy on the vaginal microbiomes of women with atrophic vaginitis","volume":"6","author":"Shen","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s40168-017-0326-y","article-title":"Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis","volume":"5","author":"Gottschick","year":"2017","journal-title":"Microbiome"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/s41522-020-00162-8","article-title":"Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth","volume":"6","author":"Feehily","year":"2020","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e00262-18","DOI":"10.1128\/mSphereDirect.00262-18","article-title":"Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis","volume":"3","author":"Deng","year":"2018","journal-title":"Msphere"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/2049-2618-1-12","article-title":"Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis","volume":"1","author":"Macklaim","year":"2013","journal-title":"Microbiome"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"904","DOI":"10.3389\/fgene.2019.00904","article-title":"Advances and challenges in metatranscriptomic analysis","volume":"10","author":"Shakya","year":"2019","journal-title":"Front. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1093\/nar\/gkv180","article-title":"Accurate read-based metagenome characterization using a hierarchical suite of unique signatures","volume":"43","author":"Freitas","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: Ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"Truong","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: Rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","article-title":"IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth","volume":"28","author":"Peng","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: A new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.3389\/fmicb.2018.03349","article-title":"SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline","volume":"9","author":"Tamames","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1186\/s13059-016-1116-8","article-title":"IMP: A pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses","volume":"17","author":"Narayanasamy","year":"2016","journal-title":"Genome Biol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Sequeira, J.C., Rocha, M., Alves, M.M., and Salvador, A.F. (2018, January 20\u201322). MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis. Proceedings of the International Conference on Practical Applications of Computational Biology & Bioinformatics, Toledo, Spain.","DOI":"10.1007\/978-3-319-98702-6_22"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nrg3129","article-title":"Experimental and analytical tools for studying the human microbiome","volume":"13","author":"Kuczynski","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1101\/gr.122800","article-title":"An assessment of gene prediction accuracy in large DNA sequences","volume":"10","author":"Guigo","year":"2000","journal-title":"Genome Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.cell.2019.07.010","article-title":"Benchmarking Metagenomics Tools for Taxonomic Classification","volume":"178","author":"Ye","year":"2019","journal-title":"Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/s41587-018-0008-8","article-title":"1520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses","volume":"37","author":"Zou","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41587-020-00777-4","article-title":"Improved metagenome binning and assembly using deep variational autoencoders","volume":"39","author":"Nissen","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"117","DOI":"10.3389\/fcimb.2020.00117","article-title":"Comparative Metagenome-Assembled Genome Analysis of \u201cCandidatus Lachnocurva vaginae\u201d, Formerly Known as Bacterial Vaginosis-Associated Bacterium\u22121 (BVAB1)","volume":"10","author":"Holm","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s40168-019-0667-9","article-title":"Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota","volume":"7","author":"Hertzberger","year":"2019","journal-title":"Microbiome"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e01594\u201320","DOI":"10.1128\/AEM.01594-20","article-title":"Novel Selective Inhibition of Lactobacillus iners by Lactobacillus-Derived Bacteriocins","volume":"86","author":"Nilsen","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.tibtech.2014.04.002","article-title":"Personalized therapy with probiotics from the host by TripleA","volume":"32","author":"Kort","year":"2014","journal-title":"Trends Biotechnol."},{"key":"ref_50","first-page":"177","article-title":"Mobiluncus gen. nov., Mobiluncus curtisii subsp. curtisii sp. nov., Mobiluncus curtisii subsp. holmesii subsp. nov., and Mobiluncus mulieris sp. nov., curved rods from the human vagina","volume":"34","author":"Spiegel","year":"1984","journal-title":"Int. J. Syst. Evol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/S0196-4399(84)80110-5","article-title":"Mobiluncus curtisii and Mobiluncus mulieris, curved motile bacteria from the human vagina","volume":"6","author":"Spiegel","year":"1984","journal-title":"Clin. Microbiol. Newsl."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"R47","DOI":"10.1016\/S0960-9822(02)01424-0","article-title":"Bacterial chemotaxis","volume":"13","author":"Webre","year":"2003","journal-title":"Curr. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"10494","DOI":"10.1074\/jbc.M111.309005","article-title":"Bacterial degradation of benzoate: Cross-regulation between aerobic and anaerobic pathways","volume":"287","author":"Valderrama","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1038\/s41396-018-0337-0","article-title":"Unveiling the role of Gardnerella vaginalis in polymicrobial bacterial vaginosis biofilms: The impact of other vaginal pathogens living as neighbors","volume":"13","author":"Castro","year":"2019","journal-title":"ISME J."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"103085","DOI":"10.1016\/j.jri.2020.103085","article-title":"Vaginal dysbiosis associated-bacteria Megasphaera elsdenii and Prevotella timonensis induce immune activation via dendritic cells","volume":"138","author":"Helgers","year":"2020","journal-title":"J. Reprod. Immunol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Huson, D.H., Beier, S., Flade, I., G\u00f3rska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H.-J., and Tappu, R. (2016). MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol., 12.","DOI":"10.1371\/journal.pcbi.1004957"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-119"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/nar\/gkh152","article-title":"ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences","volume":"32","author":"Laslett","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"D286","DOI":"10.1093\/nar\/gkv1248","article-title":"eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences","volume":"44","author":"Szklarczyk","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Eddy, S.R. (2009). A new generation of homology search tools based on probabilistic inference. Genome Informatics 2009: Genome Informatics Series Vol. 23, World Scientific.","DOI":"10.1142\/9781848165632_0019"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: Towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Ye, Y., and Doak, T.G. (2009). A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000465"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkx935","article-title":"The MetaCyc database of metabolic pathways and enzymes","volume":"46","author":"Caspi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s40168-021-01013-0","article-title":"Animalcules: Interactive microbiome analytics and visualization in R","volume":"9","author":"Zhao","year":"2021","journal-title":"Microbiome"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","article-title":"Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy","volume":"3","author":"Sieber","year":"2018","journal-title":"Nat. Microbiol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-014-0066-1","article-title":"VizBin-an application for reference-independent visualization and human-augmented binning of metagenomic data","volume":"3","author":"Laczny","year":"2015","journal-title":"Microbiome"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/3\/1621\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:11:40Z","timestamp":1760134300000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/3\/1621"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,30]]},"references-count":76,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["ijms23031621"],"URL":"https:\/\/doi.org\/10.3390\/ijms23031621","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,30]]}}}